Finally, we host meetup every Saturday morning from 9:00~10:30 PST, please join us: Saturday Meetup.
You can ask your questions via the zoom and the community can help you think through how to use Tinderbox to achieve your goals; you’ll also meet a diverse, global, group of wonderful people.
I’ve grown tremendously from my interactions with each and everyone of the community members, and not just about Tinderbox. I’ve also learned about computing theory and history, run commands, markdown, teaching, writing, moderating, communicating, child psychology, greek philosophy, engineering standards, education, script writing, choir management, architectural history, sales, metacognition, qualitative data analysis, incremental formalization, presenting, visual design, CSS, HTML, industry mapping, video production, publishing, linking and graphing, hypertext, countless application that work alongside Tinderbox (Devonthink, TextExpander, Zotero, Bookends, pandoc, Highlights, RegEx, BBEdit, iTerm…the list goes on), patience, trust, humanity, leadership, service, effective knowledge management and sense making strategies, and myself (what to improve on and do differently, stop doing, and keep doing; how to focus and listen, while keeping that puppy dog excitement), and so much more.
I’m VERY grateful. 
Oh, and
It can be, but I don’t think this a good way of thinking about prototypes.
In Tinderbox notes are like stem cells, they provide structure, function, are the foundation of “knowledge”. Every note has every attribute associated with it, whether or not the attribute has a value or note, is visible or not. The values of attributes are used by Tinderbox to perform actions and apply treatment to notes and to store values. There are both system attributes and user-generated attributes (some of my files have nearly 10,000 notes and 450+ user-generated attributes).
Tinderbox supports a concept of inheritance, meaning that in can inherit forum, function, and attribute values from the OS, the app, prototypes, etc. What a prototype is assigned to one or more notes the attribute values of the notes will inherit any changes made in the prototype; that is unless you break this inheritance for one more attribute by adjusting the value of an attribute on a note. When you do this the local value of the attribute will be safe from being overwritten while all the other attributes will still inherit from the prototype. You can always reestablish the inheritance if and when you want to.
Anyway, that’s enough for now. I’m sure you’ll come to love this app. I spend at least 80% of my day in it now.